James Shepherdson
Program: Computational and Systems Biology
Current advisor: Barak A. Cohen, PhD
Undergraduate university: Johns Hopkins University
Research summary
The transcription factor Cone-Rod Homeobox (CRX) is a master regulator of photoreceptor cell fate. Sequence variants in CRX can cause Retinitis Pigmentosa, Cone-Rod Dystrophy, and Leber Congenital Amaurosis, all inherited causes of vision loss and blindness. Several CRX variants have been reported to cause severe dominant disease through antimorphic genetic interactions with wild-type CRX, and yet these mutations are adjacent to variants which are benign or only cause mild, recessive disease. Determining which mutations in CRX are pathogenic and quantifying their effect on functional activity is prerequisite to interpreting patient variation and predicting patient phenotypes.
However, most variants in CRX are “Variants of Uncertain Significance” (VUS), meaning that insufficient clinical or functional evidence exists to determine their pathogenicity. I performed a Deep Mutational Scan (DMS) of CRX, using libraries of CRX variant sequences in a multiplexed high-throughput transcriptional reporter assay to simultaneously measure the functional consequence of nearly all possible missense variants in a single experiment. The direct product of this work includes a “look-up table” listing the functional consequence of every CRX variant on protein activity, which will be directly applicable to clinical variant classification and decision making. In addition, this work also informed on the sequence composition and characteristics of CRX and transcription factor activation domains in general.
Graduate publications
Shepherdson JL, Friedman RZ, Zheng Y, Sun C, Oh IY, Granas DM, Cohen BA, Chen S, White MA. 2024 Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors. Genome Res, 34(2):243-55.
Shepherdson JL, Hutchison K, Don DW, McGillivray G, Choi TI, Allan CA, Amor DJ, Banka S, Basel DG, Buch LD, Carere DA, Carroll R, Clayton-Smith J, Crawford A, Dunø M, Faivre L, Gilfillan CP, Gold NB, Gripp KW, Hobson E, Holtz AM, Innes AM, Isidor B, Jackson A, Katsonis P, Amel Riazat Kesh L; Genomics England Research Consortium; Küry S, Lecoquierre F, Lockhart P, Maraval J, Matsumoto N, McCarrier J, McCarthy J, Miyake N, Moey LH, Németh AH, Østergaard E, Patel R, Pope K, Posey JE, Schnur RE, Shaw M, Stolerman E, Taylor JP, Wadman E, Wakeling E, White SM, Wong LC, Lupski JR, Lichtarge O, Corbett MA, Gecz J, Nicolet CM, Farnham PJ, Kim CH, Shinawi M. 2024 Variants in ZFX are associated with an X-linked neurodevelopmental disorder with recurrent facial gestalt. Am J Hum Genet, 111(3):487-508.
Shepherdson JL, Zheng H, Amarillo IE, McAlinden A, Shinawi M. 2021 Delineation of the 1q24.3 microdeletion syndrome provides further evidence for the potential role of non-coding RNAs in regulating the skeletal phenotype. Bone, 142():115705.
King DM, Hong CKY, Shepherdson JL, Granas DM, Maricque BB, Cohen B. 2020 Synthetic and Genomic Regulatory Elements Reveal Aspects of cis-regulatory Grammar in Mouse Embryonic Stem Cells. Elife, 9():e41279.